Contacts of the helix formed by residues 332 - 355 (chain B) in PDB entry 4E2I
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLN* 4.0 0.7 - - - +
270B TRP* 5.1 6.5 - - + -
330B SER* 3.2 10.6 + - - +
331B LYS* 1.3 93.4 - - - +
333B GLN* 1.3 64.1 - - - +
334B LYS 3.2 3.4 - - - +
335B THR* 3.6 26.8 + - + +
336B ILE* 3.0 29.0 + - + +
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A THR* 5.1 7.3 + - - +
339A GLN* 3.1 24.6 + - + +
343A THR* 3.7 22.6 + - - +
289B LEU* 3.2 26.7 - - + +
293B LEU* 3.8 24.6 - - - +
327B PHE* 3.3 39.7 - - + +
328B ALA* 3.0 28.4 - - - +
330B SER* 3.6 13.0 - - - +
332B ASN* 1.3 77.7 - - - +
334B LYS* 1.3 61.1 + - - +
337B CYS* 3.6 9.5 + - - -
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Residues in contact with LYS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN* 5.2 3.2 + - - -
339A GLN* 4.6 7.2 - - + +
342A ASP* 3.7 36.9 + - + +
512A LYS* 4.9 9.7 - - - +
514A LEU* 5.8 4.5 - - - +
516A LYS* 4.7 17.6 - - - +
285B VAL* 4.2 23.6 - - + +
286B LEU* 4.6 7.6 - - + -
289B LEU* 4.3 16.4 - - + +
332B ASN* 3.2 0.6 - - - +
333B GLN* 1.3 77.6 - - - +
335B THR* 1.3 60.0 + - - +
337B CYS* 4.0 3.3 - - - +
338B GLN* 3.0 33.8 + - + +
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Residues in contact with THR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B TRP* 3.6 24.0 - - + -
332B ASN* 3.1 30.4 + - + +
334B LYS* 1.3 77.7 - - - +
336B ILE* 1.3 66.2 + - - +
338B GLN* 3.1 16.3 + - + +
339B GLN* 3.2 10.9 + - - +
331C LYS 5.9 0.4 - - - +
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.9 20.9 - - + -
269B SER 4.6 0.7 - - - +
270B TRP* 3.6 46.3 - - + +
273B VAL* 3.6 34.2 - - + +
274B THR* 5.3 1.4 + - - -
327B PHE* 3.5 25.4 - - + -
330B SER* 3.3 26.0 - - - +
332B ASN* 3.0 14.5 + - + +
335B THR* 1.3 77.0 - - - +
337B CYS* 1.3 62.6 + - - +
339B GLN* 3.6 4.7 + - - +
340B ALA* 3.5 16.3 + - - +
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Residues in contact with CYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 4.2 13.9 - - - -
285B VAL* 4.3 9.4 - - + +
288B LEU* 3.4 15.3 - - + +
289B LEU* 3.6 29.6 - - + -
292B TYR* 4.7 2.2 - - - -
327B PHE* 3.5 30.1 - - - -
333B GLN 3.6 9.4 + - - +
334B LYS* 4.3 3.4 - - - +
336B ILE* 1.3 77.5 - - - +
338B GLN* 1.3 64.5 + - - +
340B ALA* 3.3 10.2 + - - +
341B VAL* 3.0 28.6 + - - +
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Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 5.2 10.1 - - - +
285B VAL* 3.3 37.7 - - + +
334B LYS* 3.0 27.9 + - + +
335B THR* 3.1 12.5 + - + +
337B CYS* 1.3 76.7 - - - +
339B GLN* 1.3 63.6 + - - +
341B VAL* 3.1 20.3 + - - +
342B ASP* 3.0 38.4 + - - +
334C LYS* 5.3 3.5 + - - +
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Residues in contact with GLN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B TRP* 3.1 30.2 - - + +
274B THR* 4.2 8.9 + - - +
335B THR* 3.2 8.6 + - + +
336B ILE 3.9 7.6 - - - +
338B GLN* 1.3 79.5 - - - +
340B ALA* 1.3 60.8 + - - +
342B ASP* 3.2 14.4 + - + +
343B THR* 2.9 25.4 + - - +
289C LEU* 5.7 1.3 - - + +
328C ALA 5.5 0.2 - - - +
330C SER 3.2 19.0 + - - +
331C LYS 3.5 12.7 + - - -
333C GLN* 3.2 55.7 + - + +
334C LYS* 4.8 5.8 - - + +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 4.1 4.3 - - + +
274B THR* 3.9 20.8 + - - +
277B ALA* 3.5 13.9 - - + +
288B LEU* 3.4 17.7 - - + -
336B ILE 3.5 10.0 + - - +
337B CYS* 3.3 11.2 + - - +
338B GLN 3.2 0.6 - - - -
339B GLN* 1.3 79.1 - - - +
341B VAL* 1.3 63.4 + - - +
343B THR* 3.0 11.7 + - - -
344B VAL* 2.9 26.7 + - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B CYS 4.3 0.7 - - - +
283B ASP* 3.5 30.5 - - - +
284B ASP 3.1 28.7 - - - +
285B VAL* 3.6 21.3 - - + -
288B LEU* 3.9 5.6 - - + -
337B CYS 3.0 17.3 - - - +
338B GLN* 3.1 10.1 + - - +
340B ALA* 1.3 77.6 - - - +
342B ASP* 1.3 57.3 + - - +
344B VAL* 3.0 11.7 + - - +
345B LEU* 2.9 39.1 + - + +
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLN* 3.0 36.3 + - - +
339B GLN* 3.2 13.4 + - + +
341B VAL* 1.3 77.3 - - - +
343B THR* 1.3 58.4 + - - +
345B LEU* 3.8 11.5 - - - +
346B ALA* 2.8 30.0 + - - +
516B LYS* 5.9 0.2 - - - -
286C LEU* 3.7 26.2 - - + +
289C LEU* 4.3 12.5 - - + +
334C LYS* 4.0 30.1 + - + +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B THR* 3.6 27.2 - - + +
278B MET* 3.5 31.2 - - + +
339B GLN 2.9 14.4 + - - -
340B ALA 3.0 9.3 + - - -
342B ASP* 1.3 76.2 - - - +
344B VAL* 1.3 62.0 + - - +
346B ALA* 3.4 7.1 - - - +
347B LYS* 3.1 16.3 + - - +
289C LEU* 5.0 2.0 - - - +
293C LEU* 3.9 23.0 - - + +
333C GLN* 3.7 15.5 + - - +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 3.7 28.7 - - + +
278B MET* 4.3 8.5 - - - +
281B LYS* 3.6 17.0 - - - +
282B CYS 3.2 29.4 - - - +
283B ASP* 4.0 4.7 - - + +
340B ALA 2.9 21.1 + - - +
341B VAL 3.0 6.7 + - - +
343B THR* 1.3 75.5 - - - +
345B LEU* 1.3 66.4 + - - +
347B LYS* 3.1 20.0 + - + +
348B LYS* 3.3 31.4 + - - +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ASP* 3.9 29.4 - - + +
341B VAL* 2.9 30.6 + - + +
342B ASP* 4.0 10.5 - - - +
344B VAL* 1.3 77.1 - - - +
346B ALA* 1.3 57.7 + - - +
348B LYS* 3.4 15.1 + - + +
349B ARG* 2.8 30.7 + - - +
466B ASP* 4.9 1.7 - - - +
511B LYS* 4.3 30.1 - - + +
286C LEU* 4.4 20.9 - - + -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ASP 2.8 19.6 + - - +
343B THR* 3.4 12.3 - - - +
345B LEU* 1.3 75.0 - - - +
347B LYS* 1.3 65.1 + - - +
349B ARG* 3.1 9.7 + - - +
350B VAL* 3.0 29.1 + - - +
286C LEU* 3.7 22.0 - - + +
289C LEU* 4.6 6.7 - - + -
290C GLY* 3.8 17.7 - - - +
293C LEU* 5.0 1.3 - - + -
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B MET* 3.9 28.1 - - + +
343B THR 3.1 11.7 + - - +
344B VAL* 3.1 12.2 + - + +
346B ALA* 1.3 76.5 - - - +
348B LYS* 1.3 56.9 + - + +
350B VAL* 3.0 10.4 + - + +
351B ASP* 2.7 56.8 + - - +
290C GLY* 5.8 0.7 - - - -
294C GLU* 4.6 14.6 + - - +
304C LYS* 5.7 5.5 - - - +
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Residues in contact with LYS 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LYS* 3.7 24.7 + - - +
283B ASP* 4.4 12.2 - - - +
344B VAL* 3.3 35.9 + - - +
345B LEU* 3.8 17.3 - - + +
347B LYS* 1.3 81.5 - - + +
349B ARG* 1.3 64.3 + - - +
351B ASP* 4.0 8.8 - - - +
352B SER* 3.1 27.4 + - - -
466B ASP* 4.1 17.0 - - + +
467B GLN* 5.5 9.0 - - - +
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 2.8 15.1 + - - +
346B ALA* 3.1 18.4 + - - +
348B LYS* 1.3 77.1 - - - +
350B VAL* 1.3 56.3 + - - +
352B SER* 3.0 14.2 + - - -
353B LEU* 4.0 10.0 - - - +
465B ILE* 3.1 17.0 - - - +
466B ASP* 3.0 28.9 + - - -
511B LYS* 3.5 17.2 - - - +
516B LYS* 2.9 36.2 + - - +
517B ARG* 3.1 29.9 + - - +
284C ASP* 4.6 1.3 + - - -
286C LEU* 3.3 35.9 - - - +
287C LEU* 3.7 31.7 - - + +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA 3.0 16.5 + - - +
347B LYS* 3.0 10.7 + - + +
349B ARG* 1.3 77.2 - - + +
351B ASP* 1.3 62.1 + - - +
352B SER 3.1 1.8 - - - -
353B LEU* 2.9 22.6 + - - +
354B GLN* 3.1 43.2 + - + +
287C LEU* 4.7 8.3 - - + +
290C GLY* 4.0 27.1 - - - -
291C MET* 3.7 20.2 - - + +
294C GLU* 4.4 9.9 - - - +
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Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS* 2.7 53.0 + - - +
348B LYS* 3.9 7.7 + - - +
350B VAL* 1.3 78.4 - - - +
352B SER* 1.3 58.5 + - - +
353B LEU 3.0 5.1 + - - -
354B GLN* 4.5 3.5 - - - +
355B LEU* 3.3 55.9 + - + +
360B MET* 3.9 8.6 - - + +
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LYS 3.1 12.0 + - - -
349B ARG 3.0 19.6 + - - -
351B ASP* 1.3 76.3 - - - +
353B LEU* 1.3 64.0 + - - +
355B LEU 4.9 2.4 - - - +
360B MET* 4.2 20.4 - - - +
466B ASP* 3.2 37.8 + - - -
467B GLN 5.5 1.3 - - - -
517B ARG* 4.1 4.9 + - - -
519B GLN* 4.6 3.3 + - - -
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ARG 4.0 5.4 - - - +
350B VAL* 2.9 6.4 + - - +
352B SER* 1.3 88.3 - - - +
354B GLN* 1.3 68.2 + - + +
355B LEU 4.6 2.5 - - - +
517B ARG* 3.2 33.0 - - - +
519B GLN* 6.0 3.1 - - + -
287C LEU* 3.9 30.1 - - + -
291C MET* 6.3 0.9 - - - -
310C GLN* 5.0 7.4 + - - +
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Residues in contact with GLN 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B VAL* 3.1 39.3 + - + +
351B ASP* 5.0 2.0 - - - +
353B LEU* 1.3 82.5 - - + +
355B LEU* 1.3 69.7 + - + +
356B THR* 3.5 5.9 + - - +
359B GLN* 4.6 1.6 - - - +
291C MET* 4.0 11.7 - - + +
294C GLU* 3.6 20.4 + - - -
304C LYS* 3.9 22.8 - - - +
309C GLU* 4.7 7.4 - - - +
310C GLN* 3.4 41.8 + - + +
313C HIS* 5.8 2.3 - - - +
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASP* 3.3 47.2 + - + +
352B SER 4.9 0.9 - - - +
353B LEU 4.6 2.4 - - - +
354B GLN* 1.3 83.2 + - + +
356B THR* 1.3 69.6 + - - +
359B GLN* 3.4 31.2 - - + +
360B MET* 3.8 16.6 - - + +
363B ASN* 3.6 26.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il